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variantAnnotation
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
22 days ago
Stevie Pederson
• 0
0
votes
1
reply
149
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
maltethodberg
▴ 180
2
votes
3
replies
1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile
VariantAnnotation
updated 3 months ago by
Alex
• 0 • written 2.8 years ago by
Paul Shannon
▴ 470
0
votes
0
replies
167
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
3 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
5
replies
485
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
nhaus
▴ 30
0
votes
0
replies
454
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
7 months ago
Bogdan
▴ 670
2
votes
2
replies
1.5k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
549
views
Docker usage with Trio Bioconductor Package
VariantAnnotation
docker
trio
updated 11 months ago by
ATpoint
★ 4.1k • written 11 months ago by
sethberke
• 0
8 results • Page
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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